Minimally invasive medical techniques are intended to reduce the amount of tissue that is damaged during interventional procedures, thereby reducing patient recovery time, discomfort, and deleterious side effects. Such minimally invasive techniques may be performed through natural orifices in a patient anatomy or through one or more surgical incisions. Through these natural orifices or incisions clinicians may insert interventional instruments (including surgical, diagnostic, therapeutic, or biopsy instruments) to reach a target tissue location. To reach the target tissue location, a minimally invasive interventional instrument may navigate natural or surgically created passageways in anatomical systems such as the lungs, the colon, the intestines, the kidneys, the heart, the circulatory system, or the like. To assist the clinician in navigating the instrument through the passageways, models of the passageway are prepared using pre-operative or inter-operative imaging. Current systems for tracking the movement of the instrument relative to the modeled passageways are vulnerable to error because precisely locating a portion of the instrument, such as the tip, in a dense thicket of narrow anatomical passageways is often challenging. Improved systems and methods are needed for registering a portion of the instrument to the model of the anatomic passageways to track movement of the instrument relative to the model of the anatomy.